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Abraham Gihawi
Computational Biologist
Multidisciplinary bioinformatician with a keen interest in cancer and pathogen genomics. During my PhD, developed containerised computational pipelines to allow for the automated and reproducible retrieval of pathogenic sequences from within human tissue DNA sequencing data. Also formulated hypotheses as to how pathogens influence tumour biology by searching for clinical associations. Looking for a position working to extract useful insights from biological data that make a positive impact on health and lifestyle.
Academia
Senior Bioinformatics Officer
Cancer Genetics and Metagenomics
UEA
2021 - Aug 2022
This position stemmed from a successful grant application using insights obtained during my PhD. This project uses whole genome and RNA sequencing data from the Pan-Prostate Cancer Group (PPCG) to identify how microbes might be associated with aggressive prostate cancer. I am currently developing pipelines to process tumour sequence data to alongside rich clinical metadata.
PhD Computational Biology
Thesis: “Searching for Pathogens in Cancer Sequence Data”
UEA
2021 - 2017
Supervisors: Prof. Daniel Brewer, Dr. Ghanasyam Rallapalli, Dr. Richard Leggett, Dr. Rachel Hurst, Prof. Colin Cooper
In this position I developed benchmarked approaches to search for microbial nucleic acids within human tissue sequence data. I applied these pipelines to multiple datasets including Genomics England’s 100,000 Genomes Project. This has lead to characterising the microbial landscape of the tumour microenvironment. I have also investigated human and metagenomic transcriptomic data from exosomal fractions of urine from patients under investigation for prostate cancer. This has revealed some potentially impactful associations with clinical metadata and generated hypotheses regarding how pathogens interact with tumours. Additionally this work has lead to successful grant applications and intellectual property.
Technical Skills:
Proficiency in various programming languages (R, Python and Unix), Developing and applying computational pipelines (Snakemake), handling large quantities of sequencing data, containerising software, reproducible research, microbial bioinformatics, high performance computing, dimensionality reduction, version control software, metagenomic assembly, assembly of bacterial isolates, prediction of metabolic pathways, human RNA differential expression, analysis of 16S ribosomal RNA sequencing data, phylogenetics, clustering algorithms, machine learning approaches (random forest, boruta), survival analysis, submission of sequence data to public archives
Other Skills:
Scientific writing, problem solving, critical thinking, project management and organisation, presentation skills, translational research, multidisciplinary collaboration.
MSc, Cancer Therapeutics - Distinction - 80%
Project: PHLDA1 in FGFR Inhibitor Resistant Cancer
QMUL
2017 - 2015
Supervisors: Prof. Richard Grose
In this course I delved into the depths of how we can leverage the underlying science of cancer for clinical benefit. I studied a range of subjects relating to cancer including: cancer biology ablative therapies, cancer pathology, cancer pharmacology, cancer prevention and screening, molecular diagnostics and therapeutics, drug development molecular diagnostics and therapeutics, molecular targeted therapies for haematological malignancies and genomic approaches to human disease. My project involved characterising PHLDA1 which was shown to be the most significantly downregulated gene in fibroblast growth factor receptor (FGFR) inhibitor resistant endometrial cancer.
Technical Skills:
Mammalian cell culture, western blotting, 3D organotypic culture models, clonogenic assays, efficient laboratory work, analysing immunofluorescence images, searching for synergistic relationship between candidate drugs.
Other Skills:
Time management, Student representative for the course, conveying the concerns of both on-site students as well as remote leaners to faculty staff.
BSc (hons) Biomedical Science - 69%
Project: A Portable Test for Bacteria & Urobilinogen in Urine
Lincoln
2014 - 2011
Supervisor: Dr Jose Gonzalez-Rodriguez
This course, accredited by the Institute of Biomedical Science (IBMS) provided me with a base level of knowledge in the biomedical field. I read several topics including: Pharmacology, Anatomy & Physiology, Biochemistry, Molecular Biology, Genetics, Health & Disease, Microbiology, Immunology, General Good Laboratory Practice, Research Skills. Seeking to develop my scientific independence, I selected the research topic “Developing a Portable Assay for the Detection of Bacteria & Urobilinogen in Urine” for my final year project. In this project I developed assays for bacteria and urobilinogen in urine and investigated whether mobile phone cameras could accurately quantify these analytes.
Technical Skills:
Good laboratory practice, research methods, microbiological culture, gram staining, independent scientific research, microtomy, microscopy, blood cell morphology, tissue staining and histology, electrophoresis, pipetting, fluorescent in situ hybridization, latex agglutination assays.
Experience
Medical Laboratory Assistant
Royal Sussex County Hospital
Brighton
2017 - 2015
In this position I was responsible for implementing and conducting laboratory processing of samples for research studies and clinical trials. My day to day duties involved collaborating with a wide range of clinical and non-clinical staff, maintaining laboratory equipment sample processing such as centrifugation, blood smears, flow cytometry and isolation of peripheral blood mononuclear cells. One of the ways this position stimulated my interest in cancer was by carrying out a trial for the Endopredict prognostic qPCR expression assay for patients with HER2- ER+ breast cancer.
Health Advisor NHS 111
Care UK
Dorking
2015 - 2014
In this position I utilised my knowledge to assist patients with their medical concerns. I triaged them over the telephone and directed them towards the appropriate medical services. This post allowed me to witness the human element of medical care. I handled a wide range of clinical events ranging from physical trauma to mental health crises, safeguarding concerns, urinary tract infections to symptoms of metastatic cancer.
NHS Experience Placements
Princess Diana & Scunthorpe General
Grimsby & Scunthorpe
2014 - 2013
These work experience placements allowed me to witness many of the different aspects of patient care by assisting staff in a range of departments including: Radiology, Nuclear Medicine, Cardiology and Pathology (Biochemistry, Haematology, Transfusion, Andrology, Virology). This was an incredibly useful set of experiences that I feel has given me a holistic perspective on patient care.
Publications
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Genome Biology
DOI: 10.1186/s13059-019-1819-8
2019
Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst… Daniel S. Brewer
Potential for Diagnosis of Infectious Disease from the 100,000 Genomes Project Metagenomic Dataset: Recommendations for Reporting Results
Wellcome Open Research
DOI: 10.12688/wellcomeopenres.15499.1
2019
Gkikas Magiorkinis… Abraham Gihawi… Colin Cooper.
Grants
“Unraveling how bacterial infection drives the development of aggressive prostate cancer” - Prostate Cancer UK
I was a co-applicant alongside Prof. Daniel Brewer for this grant from Prostate Cancer UK to the value of £70,317. This grant provides financial support to fund a Senior Bioinformatics Officer for 18 months. This grant is responsible for my current position.
Conferences and Presentations
Presenting scientific data is something that I find valuable and I have been fortunate to be able to present to a diverse range of audiences in recent years. This includes planning and preparing outreach to schools, producing award winning scientific posters and I am an invited speaker at the International Conference on Clinical Metagenomics held in Geneva (postponed to 2021 due to the COVID-19 pandemic). Other international conferences I have attended and presented posters at include: The Human Microbiome, European Molecular Biology Laboratory Heidelberg (2018), and Bioinformatics in Cancer, virtual conference (2021)
One of my most successful presentations won a runner-up award for best poster after producing an interactive poster (code available on GitHub) and giving a talk on the content to the audience. The posters were also hosted online which attracted a wide range of participation and engagement.
Other presentations I have given include a poster presentation (code available on GitHub for a Genomics England research symposium, which included experienced scientists and project participants. Additionally, I have given talks and presented posters at our local university’s postgraduate researcher events as well as presenting frequently within my laboratory group meetings and departments bioinformatics meetings. In these bioinformatics meetings I have instigated programming challenges which I host fortnightly to enable us to discuss various aspects of scientific coding and problem solving.
Other
Peer Review: Genome Biology (BMC), Genomics (Elsevier)